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Threshold q-gram distance

The threshold q-gram distance (tqd) measures the similarity between two sequences using the concept of q-grams, and is able to capture the hapax (uniquely occurring substring) and repeat content in the sequences.

Pre-requisites

The threshold q-gram distance requires:

  • Python 3
  • g++

Installation

git clone https://github.com/AlessioMilanese/Threshold_q-gram_distance.git
cd Threshold_q-gram_distance
./setup

Note: in the following examples we assume that the python script tqd is in the system path.

Simple examples

Here is a simple example on how to obtain the tqd between two fasta files:

tqd file1.fasta file2.fasta -q 6 -threshold 1

If you want to directly input the string sequences:

tqd ATGGATCAGTC CTGGATCAGAC -q 3 -threshold 1 -strings

Parameters inputs

Usage: tqd <first_file> <second_file> [options]

Options:
   -q           INT   value of q in the q-grams[10]
   -threshold   INT   value of the threshold [1]
   -strings           set if the inputs are strings instead of files
   -pair_status FILE  file to save the pair statuses
   -verbose     INT   verbose level: 1=error, 2=warning, 3=message, 4+=debugging [2]